RetrogeneDB ID: retro_cfam_273

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:88114788..88114960(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: DPH3
• Ensembl ID: ENSCAFG00000005881
• Aliases: None
• Description: diphthamide biosynthesis 3 [Source:HGNC Symbol;Acc:27717]

Sequence

>retro_cfam_273
CCCTGCCCATGTGGGGATAACTTCTGCATTATGAAGGAAGATTTGGAGAATGGAAAGACGTAGCAATGGGACCAGCTGCT
TTGTCATTGTAAAAGTGATTTATGACAAAAAACAGTTTAGGTGTGGAGAAACAGTCCCAGCCTCTTCCATCCACAAAGAA
TTAGTTAAATGC

Alignment

ORF - retro_cfam_273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.33 %
• Parental protein coverage: 70.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PCPCGDNFCITKEDLENGE-DVATCP-SCSLIIKVIYDKDQFMCGETVPAPSTHKELVKC
          PCPCGDNFCI.KEDLENG..DVA..P.SC..I.KVIYDK.QF.CGETVPA.S.HKELVKC
Retrocopy PCPCGDNFCIMKEDLENGK<DVAMGP<SCFVIVKVIYDKKQFRCGETVPASSIHKELVKC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	0.00 RPM	4.75 RPM
SRP017611_brain	0.00 RPM	3.81 RPM
SRP017611_kidney	0.00 RPM	7.20 RPM
SRP017611_liver	0.00 RPM	1.60 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_273 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_273 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_273 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003916	2 retrocopies	retro_btau_797, retro_btau_967,
Canis familiaris	ENSCAFG00000005881	1 retrocopy	retro_cfam_273 ,
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Equus caballus	ENSECAG00000016591	1 retrocopy	retro_ecab_1095,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Felis catus	ENSFCAG00000006355	1 retrocopy	retro_fcat_656,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,